Precise timing and location of gene expression is imperative to the development and survival of an organism. Misregulation of gene expression can result in disease, developmental disorders, and cancer. Transcription of a gene can be regulated, in part, by regulating the physical accessibility of that region of DNA. In eukaryotic organisms, genomic DNA is tightly wrapped around repeating arrays of nucleosomes, effectively limiting binding by transcription factors and other regulatory proteins to that region of DNA. It has been discovered in the Widom lab that yeast discriminately position their nucleosomes, genome-wide, by encoding specific signals in their DNA that favor or disfavor nucleosome occupancy. The extent to which this is also true in multicellular eukaryotes has been questioned and is not presently known. The aim of this research is to develop a detailed understanding of the key features that govern nucleosome organization in the multicellular metazoan organism, Drosophila melanogaster. Aspects of chromatin architecture to be analyzed include intrinsic differences between heterochromatic and euchromatic loci, the genomic function of linker histone H1 containing nucleosomes; and finally, competition between nucleosomes and regulatory proteins in segmentation gene regulatory modules important for embryo development. Knowledge of these features of the Drosophila genome will advance our understanding of higher eukaryotic nucleosome positioning and transcriptional regulation.